The war was instigated by Philip of Spain to keep his enemy, France, from interfering with the Spanish army in the Netherlands and his planned invasion of England.

The war began when the Catholic League convinced King Henry III to issue an edict outlawing Protestantism and annulling Henry of Navarre's right to the throne; Henry III was possibly influenced by the royal favorite, Anne de Joyeuse.

For the first part of the war, the royalists and the Catholic League were uneasy allies against their common enemy, the Huguenots. Henry sent Joyeuse into the field against Navarre, while he himself intended to meet the approaching German and Swiss armies. At the Battle of Coutras, Navarre defeated the royal army led by Joyeuse; the duke himself was slain at the battle. It was the first victory won by the Huguenots in the battlefield. For his part, Henry III successfully prevented the junction of the German and Swiss armies. The Swiss were his allies, and had come to invade France to free him from subjection; but Henry III insisted that their invasion was not in his favor, but against him, forcing them to return home. The Germans, led by Fabien I, Burgrave of Dohna, wanted to fight against the Duke of Guise, in order to win a victory like Coutras. He recruited some of the retreating Swiss, who had no scruple fighting against Guise. But at the Battle of Vimory, Guise took the Germans by surprise, and routed them.[2]

In Paris, the glory of repelling the German and Swiss Protestants all fell to the Duke of Guise. The king's actions were viewed with contempt. They thought that the king had invited the Swiss to invade, paid them for coming, and sent them back again. The king, who had really performed the decisive part in the campaign, and expected to be honored for it, was astounded that public voice should thus declare against him. The Catholic League had put its preachers to good use. In the meantime, the governments of Normandy and Picardy were vacated by the deaths of Joyeuse and Condé. Guise demanded Normandy for himself, and Picardy for his kinsman Aumale. The king denied both requests. The Catholic League was mobilized to resist the royal appointees in these provinces. Guise was forbidden from entering the capital. Guise ignored the prohibition and entered Paris.[3] In the normal course of affairs this would have cost him his life, but the duke was popular with the masses. Further, after the Day of the Barricades, an uprising planned in part by the Spanish diplomat Bernardino de Mendoza, the king decided to flee to Blois.

After the defeat of the Spanish Armada in 1588, the king called the Estates-General in the midst of intrigue and plotting. Henri of Guise planned to assassinate the king and seize the throne, but the king struck first by having Guise killed by his guards, The Forty-Five.[4]

Open war erupted between the royalists and the Catholic League. Charles, Duke of Mayenne, Guise's younger brother, took over the leadership of the League. At the moment it seemed that he could not possibly resist his enemies. His power was effectively limited to Blois, Tours, and the surrounding districts. In these dark times the King of France finally reached out to his cousin and heir, the King of Navarre. Henry III declared that he would no longer allow Protestants to be called heretics, while the Protestants revived the strict principles of royalty and divine right. As on the other side ultra-Catholic and anti-royalist doctrines were closely associated, so on the side of the two kings the principles of tolerance and royalism were united. Henry III sought the aid of the Swiss, who were ready to join his cause. The Catholic royalists revived in their allegiance. At Pontoise the king saw himself at the head of 40,000 men. His newly recovered power may have inspired him with great designs; he planned to take Paris, in order to end the League's power once and for all.[5] The surrender of Paris seemed likely, even to the inhabitants. The preachers of the League sanctioned regicide, to avenge the murder of Guise. Jacques Clément, a fanatical Catholic monk, assassinated King Henry III at Saint-Cloud in August 1589.

With Henry III's death, the coalition broke up. Many Catholic royalists were unwilling to serve the Protestant Henry IV, and the army retreated from Paris.

In the spring, the extant Henry, Henry of Navarre (later Henry IV of France), returned to the field; he won significant victories at Ivry and Arques and laid siege to Paris (despite being greatly outnumbered), but a Spanish army under Alexander Farnese, Duke of Parma lifted the siege.

Deciding that further fighting was not worth the cost, Henry converted to Catholicism in 1593. The people of Paris were weary of war and disillusioned with the leaders of the League, and welcomed him amidst jubilation.

The war lasted several more years, as League diehards and Spanish troops continued to resist the reunification of France. But once those were dealt with, the new king Henry IV's reign inaugurated a time of commerce and peace, commonly regarded as a golden age, and he remains one of France's most beloved kings.